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#!/usr/bin/python3
"""
Read a MAF and print counts and frequencies of all n-mers
(words composed on n consecutive alignment columns)
TODO: reconcile this and maf_mapping_word_frequency.py
usage: %prog n < maf_file
"""
import string
import sys
from bx.align import maf
def __main__():
motif_len = int(sys.argv[1])
big_map = {}
total = 0
maf_reader = maf.Reader(sys.stdin)
for m in maf_reader:
texts = [c.text.upper() for c in m.components]
for i in range(m.text_size - motif_len):
motif = string.join(text[i : i + motif_len] for text in texts)
if motif in big_map:
big_map[motif] += 1
else:
big_map[motif] = 1
total += 1
items = sorted(zip(big_map.values(), big_map.keys()))
items.reverse()
for count, motif in items:
print("%d\t%0.10f\t%s" % (count, count / total, motif))
if __name__ == "__main__":
__main__()
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